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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

ALKBH5 Gene

protein-coding   GIFtS: 43
GCID: GC17P018086

alkB, alkylation repair homolog 5 (E. coli)

(Previous name: oxoglutarate and iron-dependent oxygenase domain containing...)
(Previous symbol: OFOXD1)
 Explore 2 diseases affiliated with
ALKBH5 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for ALKBH5    

Aliases
for ALKBH5 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
AlkB, Alkylation Repair Homolog 5 (E. Coli)1 2     FLJ203081
OFOXD11 2 3     OFOXD2
ABH52 3 5     Probable Alpha-Ketoglutarate-Dependent Dioxygenase ABH52
Oxoglutarate And Iron-Dependent Oxygenase Domain Containing1 2     RNA Demethylase ALKBH52
Alkylated DNA Repair Protein AlkB Homolog 52 3     EC 1.14.11.-3
Alpha-Ketoglutarate-Dependent Dioxygenase AlkB Homolog 52 3     

External Ids:    HGNC: 259961   Entrez Gene: 548902   Ensembl: ENSG000000915427   OMIM: 6133035   UniProtKB: Q6P6C23   

Export aliases for ALKBH5 gene to outside databases

Previous GC identifers: GC17P018031 GC17P017840


Summaries
for ALKBH5 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
UniProtKB/Swiss-Prot: ALKB5_HUMAN, Q6P6C2
Function: Dioxygenase that demethylates RNA by oxidative demethylation: specifically demethylates N(6)-methyladenosine
(m(6)A) RNA, the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Requires molecular
oxygen, alpha-ketoglutarate and iron. Demethylation of m(6)A mRNA affects mRNA processing and export and is required
for spermatogenesis




Genomic Views
for ALKBH5 gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000017.10  NC_018928.1  NT_010718.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ALKBH5 gene promoter:
         Pax-5   HTF   Pax-2   Pax-2a   XBP-1   Tal-1beta   Max   HEN1   ITF-2   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: ALKBH5 promoter sequence
   Search SABiosciences Chromatin IP Primers for ALKBH5

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ALKBH5


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 17p11.2|17p11.2   Ensembl cytogenetic band:  17p11.2   HGNC cytogenetic band: 17p11.2

ALKBH5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ALKBH5 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P018086:  view genomic region     (about GC identifiers)

Start:
 18,086,392 bp from pter      End:
 18,113,268 bp from pter
Size:
 26,877 bases      Orientation:
 plus strand

Proteins
for ALKBH5 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: ALKB5_HUMAN, Q6P6C2 (See protein sequence)
Recommended Name: RNA demethylase ALKBH5  
Size: 394 amino acids; 44256 Da
Cofactor: Binds 1 Fe(2+) ion per subunit (By similarity)
Subcellular location: Nucleus speckle
Sequence caution: Sequence=BAA91078.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: B4DVJ4 D3DXC6 Q9NXD6
Alternative splicing: 3 isoforms:  Q6P6C2-2   Q6P6C2-1   Q6P6C2-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for ALKBH5: NX_Q6P6C2

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q6P6C2

    • ALKBH5 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_060228.3  
    ENSEMBL proteins: 
     ENSP00000468116   ENSP00000382091  

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    Uscn Proteins for ALKBH5

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0016021integral to membrane ----
    GO:0016607nuclear speck IDA--


    ALKBH5 for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for ALKBH5 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    ALKBH5 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR005123 Oxoglu/Fe-dep_dioxygenase

    Graphical View of Domain Structure for InterPro Entry Q6P6C2

    ProtoNet protein and cluster: Q6P6C2

    UniProtKB/Swiss-Prot: ALKB5_HUMAN, Q6P6C2
    Similarity: Belongs to the alkB family


    Function
    for ALKBH5 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         UniProtKB/Swiss-Prot: ALKB5_HUMAN, Q6P6C2
    Function: Dioxygenase that demethylates RNA by oxidative demethylation: specifically demethylates N(6)-methyladenosine
    (m(6)A) RNA, the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Requires molecular
    oxygen, alpha-ketoglutarate and iron. Demethylation of m(6)A mRNA affects mRNA processing and export and is required
    for spermatogenesis
    Induction: By hypoxia, directly activated by HIF1A. Expression is regulated by PRMT7

    Enzyme Number (IUBMB): EC 1.14.11.-1

    miRNA
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    hsa-miR-302d hsa-miR-520e hsa-miR-3607-3p hsa-miR-193a-3p hsa-miR-1197 hsa-miR-890 hsa-miR-372 hsa-miR-3122
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    Inhib. RNA
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    Gene Editing
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    Clone
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    In Situ Assay
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    Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen IEA--
    GO:0016706oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors IDA--
    GO:0035515oxidative RNA demethylase activity IDA--
    GO:0046872metal ion binding IEA--


    ALKBH5 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for ALKBH5:
     Increased gamma-H2AX phosphory 


    Pathways & Interactions
    for ALKBH5 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for ALKBH5

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    3 Interacting proteins for ALKBH5 (ENSP000003820914) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SIRT5ENSP000003685524STRING: ENSP00000368552
    ELAVL1ENSP000003852694STRING: ENSP00000385269
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    Gene Ontology (GO): 5/6 biological process terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001666response to hypoxia IDA--
    GO:0006397mRNA processing IMP--
    GO:0006406mRNA export from nucleus IMP--
    GO:0007283spermatogenesis ISS--
    GO:0030154cell differentiation IEA--


    ALKBH5 for ontologies           About GeneDecksing



    Drugs & Compounds
    for ALKBH5 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for ALKBH5
    Search CenterWatch for drugs/clinical trials and news about ALKBH5 / ALKB5 

    Transcripts
    for ALKBH5 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for ALKBH5 gene: 
    NM_017758.3  

    Unigene Cluster for ALKBH5:

    AlkB, alkylation repair homolog 5 (E. coli)
    Hs.744130  [show with all ESTs]
    Unigene Representative Sequence: NM_017758
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000541285 ENST00000399138(uc010cpw.3) ENST00000490106

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    hsa-miR-302d hsa-miR-520e hsa-miR-3607-3p hsa-miR-193a-3p hsa-miR-1197 hsa-miR-890 hsa-miR-372 hsa-miR-3122
    SwitchGear 3'UTR luciferase reporter plasmid: ALKBH5 3' UTR sequence
    Inhib. RNA
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    Clone
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    Additional cDNA sequence: 

    AK000129.1 AK000315.1 AK025817.1 AK301107.1 AK311161.1 AK311511.1 AL137263.1 BC062339.1 

    10 DOTS entries:

    DT.91756074  DT.450045  DT.101971120  DT.95276932  DT.101984043  DT.100801733  DT.120974994  DT.75123302 
    DT.97847646  DT.95335833 

    24/398 AceView cDNA sequences (see all 398):

    D81994 AI038248 CA390702 AI282174 AI363416 AW674394 AW237118 AI917196 
    BM708716 CA311404 AW338389 BI793209 BM424205 BM757740 BU955890 BG056918 
    AW271663 AI085647 AK000129 F31906 CB142278 BP345833 BF726683 AK025817 

    GeneLoc Exon Structure


    Expression
    for ALKBH5 gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    ALKBH5 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CATCCAAGGC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image
    See ALKBH5 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ALKBH5

    SOURCE GeneReport for Unigene cluster: Hs.744130

    UniProtKB/Swiss-Prot: ALKB5_HUMAN, Q6P6C2
    Tissue specificity: Widely expressed, with highest expression in lung, followed by testis, pancreas, spleen and ovary

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    In Situ
    Assay Products:     
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    Orthologs
    for ALKBH5 gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    This gene was present in the common ancestor of eukaryotes.

    Orthologs for ALKBH5 gene from 7/18 species (see all 18)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia Alkbh51 , 5 alkB, alkylation repair homolog 5 (E. coli)1, 5 91.46(n)1
    97.21(a)1    		   11 (37.81 cM)5
    2684201  NM_172943.41  NP_766531.21 
     605363815 
    chicken
    (Gallus gallus)    		 Aves ALKBH51 alkB, alkylation repair homolog 5 (E. coli) 78.35(n)
    86.25(a)    		   770703  XM_001233462.2  XP_001233463.1 
    lizard
    (Anolis carolinensis)    		 Reptilia ALKBH56
    		 --
    		 82(a)
    		 1 ↔ 1
    		 GL343618.1(20374-32751)
    African clawed frog
    (Xenopus laevis)    		 Amphibia 480482982   -- 84.87(n)    48048298 
    zebrafish
    (Danio rerio)    		 Actinopterygii CK147300.12   -- 78.84(n)    CK147300.1 
    thale cress
    (Arabidopsis thaliana)    		 eudicotyledons AT1G147106
    AT1G489806
    (see all 6)    		 hydroxyproline-rich glycoprotein-like protein
    2-oxoglutarate (2OG) and Fe(II)-dependent oxygenas...
    (see all 6)    		 7(a)
    19(a)
    (see all 6)    		 many → 1
    many → 1
    (see all 6)    		 1(5061866-5065178)
    1(18118017-18120667)
    rice
    (Oryza sativa)    		 Liliopsida --
    --
    (see all 5)    		 hydroxyproline-rich glycoprotein family protein, p...
    oxidoreductase, 2OG-Fe oxygenase family protein, p...
    (see all 5)    		 9(a)
    14(a)
    (see all 5)    		 many → 1
    many → 1
    (see all 5)    		 3(7328101-7334051)
    5(19463126-19466464)


    ENSEMBL Gene Tree for ALKBH5 (if available)
    TreeFam Gene Tree for ALKBH5 (if available) 

    Paralogs
    for ALKBH5 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    		  --

    Genomic Variants
    for ALKBH5 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/450 NCBI SNPs in ALKBH5 are shown (see all 450)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 17 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs739808161,2
    		C,--18084876(+) AGCGGC/TTTCTT 1 -- us2k12Minor allele frequency- T:0.10WA 120
    rs1510815931,2
    		--18084904(+) GTTGAA/GCCAAA 1 -- us2k10--------
    rs1154223771,2
    		F,--18084999(+) TGCTCT/CTGAGC 1 -- us2k11Minor allele frequency- C:0.02WA 118
    rs1813497651,2
    		--18085182(+) CCTCAC/TTGAAT 1 -- us2k10--------
    rs9973151,2
    		C,F,A,H,--18085286(-) GCCACT/CGCGCC 1 -- us2k110Minor allele frequency- C:0.14NS EA NA WA CSA 657
    rs1860185791,2
    		--18085304(+) TGTAAC/TCCCAG 1 -- us2k10--------
    rs1909419511,2
    		--18085469(+) GTGTGA/GGAGGA 1 -- us2k10--------
    rs1398680521,2
    		--18085495(+) AGGTCA/GAGATT 1 -- us2k10--------
    rs1168163261,2
    		F,--18085700(+) TACAGG/AATGAG 1 -- us2k11Minor allele frequency- A:0.03WA 118
    rs1498366601,2
    		--18085868(+) TTGGAG/TCCCTC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for ALKBH5 (18086392 - 18113268 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for ALKBH5
         1 Inversion: 0495

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    Disorders / Diseases
    for ALKBH5 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    ALKBH5 for disorders           About GeneDecksing

    OMIM gene information: 613303    OMIM disorders: --

    2 diseases for ALKBH5:    About MalaCards
    smith-magenis syndrome    hypoxia


    Export disorders for ALKBH5 gene to outside databases

    Publications
    for ALKBH5 gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for ALKBH5 gene, integrated from 9 sources (see all 19):
    (articles sorted by number of sources associating them with ALKBH5)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Human AlkB homologue 5 is a nuclear 2-oxoglutarate de pendent oxygenase and a direct target of hypoxia-inducible factor 1I+ (HIF-1I+). (PubMed id 21264265)1, 2 Thalhammer A....Pollard P.J. (2011)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Genes in a refined Smith-Magenis syndrome critical deletion interval on chromosome 17p11.2 and the syntenic region of the mouse. (PubMed id 11997338)1, 3 Bi W....Lupski J.R. (2002)
    5. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. (PubMed id 23177736)2 Zheng G.... He C. (2013)
    6. Protein arginine methyltransferase 7 regulates cellular response to DNA damage by methylating promoter histones H2A and H4 of the polymerase delta catalytic subunit gene, POLD1. (PubMed id 22761421)2 Karkhanis V.... Sif S. (2012)
    7. Functional dissection of lysine deacetylases reveals t hat HDAC1 and p300 regulate AMPK. (PubMed id 22318606)1 Lin Y.Y....Boeke J.D. (2012)
    8. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    9. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    10. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)

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    Genome Databases showing ALKBH5 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 54890 HGNC: 25996 AceView: FLJ20308 Ensembl:ENSG00000091542 euGenes: HUgn54890
    ECgene: ALKBH5 H-InvDB: ALKBH5

    Other Databases showing ALKBH5 gene

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    Specialized Databases showing ALKBH5 gene

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    PharmGKB entry for ALKBH5 Pharmacogenomics, SNPs, Pathways

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